The scale of biological studies is rapidly evolving and biological phenomena are now observed at both super-high resolution and with genome- and organism- wide perspectives. To rise to these challenges, we must train the new generation of students to develop a broad and interdisciplinary knowledge of modern biology and experimental approaches in a highly collaborative environment. The training program in Molecules, Cells, and Organisms (MCO) is a cross- departmental doctoral training program located in the Faculty of Arts and Sciences at the Cambridge Campus of Harvard University. This highly innovative program establishes the foundation for students to become the next- generation biologists. MCO faculty mentors represent all fields of modern biology, from biophysics, structural biology and microbiology, to developmental and regenerative biology, neurobiology and genomics. Collaborating departments include Molecular and Cellular Biology, Chemistry and Chemical Biology, Organismic and Evolutionary Biology, Stem Cell and Regenerative Biology, and Physics. Through its structure of core course requirements, quantitative biology courses, journal club, nanocourses, lab rotations, seminars, hands-on model systems workshops, scientific colloquia and retreats, the MCO program exposes its trainees to the full scope of research options available to modern biologists today, and helps them develop outstanding reasoning skills and creativity, as well as oral and written communication. As the advanced field of biological analysis is now attracting scientists from all disciplines, the MCO program is designed to meet the challenge of training that combines the methods of chemistry, physics, mathematics and informatics with new concepts of cellular and molecular biology.